Hey everyone,

I have a RNASeq dataset, with three variables - Time Point (1,10,100), Drug Concentration (0,0.001,0.1) and Cell Line (LineA, LineB, LineC). Therefore, I have been working with the design: ~Time.Point*Cell.line*Drug.

My question is, according with the interactions section of DESeq2 vignette & example 3 from results function, to get the comparison between 1 and 10 days in Time Point, at the baseline drug concentration (0), for Cell.Line B, I should do:

results(dds, contrast=list( c("Time.Point_10_vs_1","Cell.LineBTime.Point10") ))

However, if i want to get the log2FC after shrinkage, do I need to reorganize the levels (put Cell.LineB as reference level) and then run nbinomWaldTest? Or is there another way to do this?

Thanks in advance

I think the simpler way to do it is to make a new column of conc_time_tissue all stuck together, and make that column your design.

Then you can easily compare one subset of samples to another.